Frontal cortices were removed and crosslinked, nuclei extracted and chromatin sonicated and clarified. MeCP2-Chromatin complexes were isolated with the indicated antibodies. End Repair and 5' Phosphorylation reactions were incubated for 30 minutes at room temperature. DNA samples were then purified, DNA was eluted with Qiagen EB buffer. A single dA overhang was added to the 3' ends of DNA fragments (New England Biolabs). Illumina adaptors were ligated and products were then purified. Adaptor ligated libraries were PCR amplified and barcoded by custom indexing primers. PCR amplified libraries were size selected and quantified using Qubit HS DNA assay and average sizes determined by using Agilent HS DNA assay chips (Thermo Fisher). Library pool was sequenced paired-end 75 on HiSeq 2500 (Illumina).